feat(kugetsu): add lock mechanism for worktree coordination

Add lock mechanism to prevent concurrent access to worktrees:
- Add LOCKS_DIR constant (~/.kugetsu/locks)
- Add acquire_lock() - acquires lock file with PID, session_id, timestamp
- Add release_lock() - releases lock if held by current process
- Add release_all_locks() - releases all locks for a session
- Add check_lock() - check if issue is locked
- Modify cmd_start to acquire lock before creating worktree
- Modify cmd_destroy to release lock when destroying session
- Add trap for cleanup on EXIT/INT/TERM

Lock files named after issue ref. Stale lock detection: if PID
no longer exists, lock is considered stale.

Fixes #71

skills/kugetsu/SKILL.md

@@ -47,6 +47,7 @@ A default config file is created during `kugetsu init` with commented examples:
 | Variable | Default | Description |
 |----------|---------|-------------|
 | `MAX_CONCURRENT_AGENTS` | 3 | Maximum number of concurrent dev agents |
+| `KUGETSU_TEMP_DIR` | `~/.local/share/opencode/tool-output` | Temp directory for subagent tool output (useful in headless environments where /tmp is restricted) |
 
 ### Environment Variables for Agents
 

skills/kugetsu/scripts/kugetsu

@@ -9,7 +9,10 @@ INDEX_FILE="$KUGETSU_DIR/index.json"
 NOTIFICATIONS_FILE="$KUGETSU_DIR/notifications.json"
 LOGS_DIR="$KUGETSU_DIR/logs"
 ENV_DIR="${ENV_DIR:-$KUGETSU_DIR/env}"
+QUEUE_FILE="$KUGETSU_DIR/queue.json"
+LOCKS_DIR="$KUGETSU_DIR/locks"
 MAX_CONCURRENT_AGENTS="${MAX_CONCURRENT_AGENTS:-3}"
+POLL_INTERVAL="${POLL_INTERVAL:-600}"
 
 # Load user config overrides (~/.kugetsu/config)
 if [ -f "$KUGETSU_DIR/config" ]; then
@@ -56,6 +59,87 @@ count_active_dev_sessions() {
     echo "$count"
 }
 
+acquire_lock() {
+    local issue_ref="$1"
+    local session_id="$2"
+    local lock_file="$LOCKS_DIR/${issue_ref//[^a-zA-Z0-9._-]/_}.lock"
+    
+    mkdir -p "$LOCKS_DIR"
+    
+    if [ -f "$lock_file" ]; then
+        local lock_pid=$(cat "$lock_file" 2>/dev/null | cut -d: -f1)
+        local lock_session=$(cat "$lock_file" 2>/dev/null | cut -d: -f2)
+        
+        if [ -n "$lock_pid" ] && ! kill -0 "$lock_pid" 2>/dev/null; then
+            echo "Stale lock detected, removing..."
+            rm -f "$lock_file"
+        elif [ "$lock_session" = "$session_id" ]; then
+            echo "Already holding lock for $issue_ref"
+            return 0
+        else
+            echo "Error: $issue_ref is locked by session $lock_session (PID $lock_pid)" >&2
+            return 1
+        fi
+    fi
+    
+    echo "${BASHPID}:${session_id}:$(date +%s)" > "$lock_file"
+    echo "Lock acquired for $issue_ref: $lock_file"
+    return 0
+}
+
+release_lock() {
+    local issue_ref="$1"
+    local lock_file="$LOCKS_DIR/${issue_ref//[^a-zA-Z0-9._-]/_}.lock"
+    
+    if [ ! -f "$lock_file" ]; then
+        return 0
+    fi
+    
+    local lock_pid=$(cat "$lock_file" 2>/dev/null | cut -d: -f1)
+    
+    if [ "$lock_pid" = "$BASHPID" ]; then
+        rm -f "$lock_file"
+        echo "Lock released for $issue_ref"
+    else
+        echo "Error: Cannot release lock held by PID $lock_pid (current: $BASHPID)" >&2
+        return 1
+    fi
+}
+
+release_all_locks() {
+    local session_id="$1"
+    if [ ! -d "$LOCKS_DIR" ]; then
+        return 0
+    fi
+    for lock_file in "$LOCKS_DIR"/*.lock; do
+        [ -f "$lock_file" ] || continue
+        local lock_session=$(cat "$lock_file" 2>/dev/null | cut -d: -f2)
+        if [ "$lock_session" = "$session_id" ]; then
+            rm -f "$lock_file"
+            echo "Released stale lock: $(basename "$lock_file")"
+        fi
+    done
+}
+
+check_lock() {
+    local issue_ref="$1"
+    local lock_file="$LOCKS_DIR/${issue_ref//[^a-zA-Z0-9._-]/_}.lock"
+    
+    if [ -f "$lock_file" ]; then
+        local lock_pid=$(cat "$lock_file" 2>/dev/null | cut -d: -f1)
+        local lock_session=$(cat "$lock_file" 2>/dev/null | cut -d: -f2)
+        
+        if [ -n "$lock_pid" ] && ! kill -0 "$lock_pid" 2>/dev/null; then
+            echo "Stale lock detected, removing..."
+            rm -f "$lock_file"
+            return 1
+        fi
+        echo "Locked by session $lock_session (PID $lock_pid)"
+        return 0
+    fi
+    return 1
+}
+
 usage() {
     cat << 'EOF'
 kugetsu - OpenCode Session Manager (Issue-Driven)
@@ -563,8 +647,10 @@ cmd_delegate() {
     mkdir -p "$LOGS_DIR"
     local log_file="$LOGS_DIR/delegate-$(date +%s).log"
     
+    local temp_dir="${KUGETSU_TEMP_DIR:-$HOME/.local/share/opencode/tool-output}"
+    
     mkdir -p "$ENV_DIR"
-    local env_sh="set -a; "
+    local env_sh="set -a; export KUGETSU_TEMP_DIR='$temp_dir'; "
     if [ -f "$ENV_DIR/pm-agent.env" ]; then
         env_sh="${env_sh}source '$ENV_DIR/pm-agent.env'; "
     elif [ -f "$ENV_DIR/default.env" ]; then
@@ -593,6 +679,116 @@ cmd_logs() {
     done
 }
 
+init_queue() {
+    if [ ! -f "$QUEUE_FILE" ]; then
+        cat > "$QUEUE_FILE" << 'EOF'
+{
+  "dev_followups": [],
+  "user_interrupts": [],
+  "background": []
+}
+EOF
+    fi
+}
+
+cmd_queue() {
+    local action="${1:-}"
+    
+    init_queue
+    
+    case "$action" in
+        ""|"list")
+            local total=0
+            echo "Queue status:"
+            for tier in dev_followups user_interrupts background; do
+                local count=$(python3 -c "import json; d=json.load(open('$QUEUE_FILE')); print(len(d.get('$tier', [])))" 2>/dev/null || echo 0)
+                total=$((total + count))
+                if [ "$count" -eq 0 ]; then
+                    echo "  $tier (0): (empty)"
+                else
+                    echo "  $tier ($count):"
+                    python3 -c "import json, sys; d=json.load(open('$QUEUE_FILE')); [print(f'    [{t[\"id\"]}] {t[\"message\"][:60]}') for t in d.get('$tier', [])]" 2>/dev/null || echo "    (error reading)"
+                fi
+            done
+            echo "Total queued: $total"
+            ;;
+        "enqueue")
+            local tier="${2:-}"
+            local message="${3:-}"
+            if [ -z "$tier" ] || [ -z "$message" ]; then
+                echo "Usage: kugetsu queue enqueue <tier> <message>" >&2
+                echo "  tier: dev_followups, user_interrupts, or background" >&2
+                exit 1
+            fi
+            if [[ ! "$tier" =~ ^(dev_followups|user_interrupts|background)$ ]]; then
+                echo "Error: Invalid tier '$tier'" >&2
+                echo "  Valid tiers: dev_followups, user_interrupts, background" >&2
+                exit 1
+            fi
+            local id="qe-$(date +%s)-$$"
+            python3 << EOF
+import json
+with open('$QUEUE_FILE', 'r') as f:
+    d = json.load(f)
+d.setdefault('$tier', []).append({
+    'id': '$id',
+    'message': '$message',
+    'created': '$(date -Iseconds)'
+})
+with open('$QUEUE_FILE', 'w') as f:
+    json.dump(d, f, indent=2)
+print('Enqueued to $tier: [$id] $message')
+EOF
+            ;;
+        "dequeue")
+            local tier="${2:-}"
+            local result=$(python3 << EOF
+import json
+with open('$QUEUE_FILE', 'r') as f:
+    d = json.load(f)
+tiers = ['dev_followups', 'user_interrupts', 'background'] if not '$tier' else ['$tier']
+for t in tiers:
+    if d.get(t) and len(d[t]) > 0:
+        task = d[t].pop(0)
+        with open('$QUEUE_FILE', 'w') as f:
+            json.dump(d, f, indent=2)
+        print(f'{t}|{task["id"]}|{task["message"]}')
+        break
+else:
+    print('Queue empty')
+EOF
+)
+            if [ "$result" = "Queue empty" ]; then
+                echo "$result"
+                exit 1
+            fi
+            echo "$result"
+            ;;
+        "clear")
+            cat > "$QUEUE_FILE" << 'EOF'
+{
+  "dev_followups": [],
+  "user_interrupts": [],
+  "background": []
+}
+EOF
+            echo "Queue cleared"
+            ;;
+        *)
+            echo "Usage: kugetsu queue <list|enqueue|dequeue|clear>" >&2
+            echo "" >&2
+            echo "Commands:" >&2
+            echo "  list                    Show queue status" >&2
+            echo "  enqueue <tier> <msg>  Add task to queue" >&2
+            echo "  dequeue [tier]         Remove and return next task" >&2
+            echo "  clear                   Clear all queued tasks" >&2
+            echo "" >&2
+            echo "Tiers: dev_followups, user_interrupts, background" >&2
+            exit 1
+            ;;
+    esac
+}
+
 cmd_env() {
     local action="${1:-}"
     local agent_type="${2:-}"
@@ -695,12 +891,16 @@ cmd_env() {
 
 cmd_doctor() {
     local fix=false
+    local fix_permissions=false
     
     while [ $# -gt 0 ]; do
         case "$1" in
             --fix)
                 fix=true
                 ;;
+            --fix-permissions)
+                fix_permissions=true
+                ;;
             *)
                 ;;
         esac
@@ -798,6 +998,52 @@ cmd_doctor() {
             fi
         fi
     fi
+    
+    if [ "$fix_permissions" = true ]; then
+        echo ""
+        echo "Fixing session permissions..."
+        fix_session_permissions
+    fi
+}
+
+fix_session_permissions() {
+    local opencode_db="${OPENCODE_DB:-$HOME/.opencode/opencode.db}"
+    
+    if [ ! -f "$opencode_db" ]; then
+        echo "[ERROR] opencode database not found: $opencode_db"
+        return 1
+    fi
+    
+    local base_session_id=$(get_base_session_id)
+    local pm_agent_session_id=$(get_pm_agent_session_id)
+    
+    local PERMISSION_JSON='[{"permission":"question","pattern":"*","action":"deny"},{"permission":"plan_enter","pattern":"*","action":"deny"},{"permission":"plan_exit","pattern":"*","action":"deny"},{"permission":"external_directory","pattern":"*","action":"allow"}]'
+    
+    if [ -n "$base_session_id" ] && [ "$base_session_id" != "null" ]; then
+        echo "Updating base session permissions: $base_session_id"
+        python3 -c "
+import sqlite3
+conn = sqlite3.connect('$opencode_db')
+cursor = conn.cursor()
+cursor.execute(\"UPDATE session SET permission = ? WHERE id = ?\", ('$PERMISSION_JSON', '$base_session_id'))
+conn.commit()
+print('[OK] Base session permissions updated')
+"
+    fi
+    
+    if [ -n "$pm_agent_session_id" ] && [ "$pm_agent_session_id" != "null" ] && [ "$pm_agent_session_id" != "None" ]; then
+        echo "Updating PM agent session permissions: $pm_agent_session_id"
+        python3 -c "
+import sqlite3
+conn = sqlite3.connect('$opencode_db')
+cursor = conn.cursor()
+cursor.execute(\"UPDATE session SET permission = ? WHERE id = ?\", ('$PERMISSION_JSON', '$pm_agent_session_id'))
+conn.commit()
+print('[OK] PM agent session permissions updated')
+"
+    fi
+    
+    echo "Session permissions fix complete"
 }
 
 DEBUG_MODE=false
@@ -1052,6 +1298,8 @@ EOF
     echo "Initialization complete!"
     echo "- Base session: $new_session_id"
     echo "- PM agent: ${new_pm_session_id:-created by hermes}"
+    
+    fix_session_permissions
 }
 
 cmd_start() {
@@ -1097,6 +1345,14 @@ cmd_start() {
     fi
 
     local worktree_path=$(issue_ref_to_worktree_path "$issue_ref")
+    
+    trap 'release_lock "$issue_ref" 2>/dev/null; exit' EXIT INT TERM
+    
+    if ! acquire_lock "$issue_ref" "$base_session_id"; then
+        echo "Error: Could not acquire lock for '$issue_ref'" >&2
+        exit 1
+    fi
+    
     create_worktree "$issue_ref"
 
     local session_file="$(issue_ref_to_filename "$issue_ref").json"
@@ -1163,6 +1419,8 @@ cmd_start() {
 
     echo "Session started for '$issue_ref': $new_session_id"
     echo "Worktree: $worktree_path"
+    
+    release_lock "$issue_ref"
 }
 
 cmd_continue() {
@@ -1416,6 +1674,7 @@ cmd_destroy() {
 
     if [ "$force" = true ]; then
         remove_worktree_for_issue "$target"
+        release_lock "$target" 2>/dev/null || true
         rm -f "$session_path"
         remove_issue_from_index "$target"
         echo "Session for '$target' destroyed"
@@ -1425,6 +1684,7 @@ cmd_destroy() {
         read reply
         if [ "$reply" = "y" ] || [ "$reply" = "Y" ]; then
             remove_worktree_for_issue "$target"
+            release_lock "$target" 2>/dev/null || true
             rm -f "$session_path"
             remove_issue_from_index "$target"
             echo "Session for '$target' destroyed"
@@ -1469,6 +1729,9 @@ main() {
         server)
             cmd_server "$@"
             ;;
+        queue)
+            cmd_queue "$@"
+            ;;
         env)
             cmd_env "$@"
             ;;

skills/kugetsu/tests/test-kugetsu-v2.sh

@@ -634,9 +634,70 @@ else
 fi
 echo ""
 
+# Test E7: KUGETSU_TEMP_DIR is exported in cmd_delegate
+echo "--- Test: KUGETSU_TEMP_DIR export in cmd_delegate ---"
+if grep -q "KUGETSU_TEMP_DIR" "$KUGETSU" && grep -q "export KUGETSU_TEMP_DIR" "$KUGETSU"; then
+    pass "KUGETSU_TEMP_DIR is exported to delegated agents"
+else
+    fail "KUGETSU_TEMP_DIR not found in cmd_delegate export"
+fi
+echo ""
+
 # Cleanup env files
 rm -rf ~/.kugetsu/env 2>/dev/null || true
 
+# Test E7: fix_session_permissions function exists
+echo "--- Test: fix_session_permissions function exists ---"
+if grep -q "fix_session_permissions()" "$KUGETSU"; then
+    pass "fix_session_permissions function exists"
+else
+    fail "fix_session_permissions function not found"
+fi
+echo ""
+
+# Test E8: cmd_doctor --fix-permissions flag is recognized
+echo "--- Test: cmd_doctor --fix-permissions flag ---"
+OUTPUT=$($KUGETSU doctor --fix-permissions 2>&1 || true)
+if echo "$OUTPUT" | grep -q -E "(Fixing session permissions|Session permissions fix complete|opencode database not found)"; then
+    pass "cmd_doctor --fix-permissions flag is recognized"
+else
+    fail "cmd_doctor --fix-permissions not recognized: $OUTPUT"
+fi
+echo ""
+
+# Test E9: fix_session_permissions has valid permission JSON
+echo "--- Test: fix_session_permissions has valid permission JSON ---"
+PERMISSION_JSON='[{"permission":"question","pattern":"*","action":"deny"},{"permission":"plan_enter","pattern":"*","action":"deny"},{"permission":"plan_exit","pattern":"*","action":"deny"},{"permission":"external_directory","pattern":"*","action":"allow"}]'
+if python3 -c "import json; json.loads('$PERMISSION_JSON')" 2>/dev/null; then
+    pass "fix_session_permissions has valid permission JSON"
+else
+    fail "fix_session_permissions permission JSON is invalid"
+fi
+echo ""
+
+# Test E10: fix_session_permissions SQL UPDATE syntax is valid
+echo "--- Test: fix_session_permissions SQL UPDATE syntax ---"
+if python3 -c "
+import sqlite3
+conn = sqlite3.connect(':memory:')
+cursor = conn.cursor()
+cursor.execute('CREATE TABLE session (id TEXT, permission TEXT)')
+cursor.execute('INSERT INTO session (id, permission) VALUES (?, ?)', ('test_id', 'original'))
+cursor.execute('UPDATE session SET permission = ? WHERE id = ?', ('$PERMISSION_JSON', 'test_id'))
+conn.commit()
+cursor.execute('SELECT permission FROM session WHERE id = ?', ('test_id',))
+result = cursor.fetchone()
+if result and 'external_directory' in result[0]:
+    print('OK')
+else:
+    print('FAIL')
+" 2>/dev/null | grep -q OK; then
+    pass "fix_session_permissions SQL UPDATE syntax is valid"
+else
+    fail "fix_session_permissions SQL UPDATE syntax failed"
+fi
+echo ""
+
 # Cleanup
 cleanup